After multiple updates, maverick development, various stuff installed, messing with grub, my Ubuntu is quite broken.

More specifically:

  • when it starts, it wants to check / for errors. Then it says that it has errors, and it wants me to choose if I want to abort, ignore, or try to fix. It can't fix them, but if I choose to ignore, it just starts.

  • Transmission occupies the whole screen (above the panels), and I can't minimize it, even whith alt+space + minimize (or unmaximize). The only way to bring my panels back is to close the Transmission window.

  • When I start the pc, the bottom panel is empty, and I need to put the panel items back every time.

Now I realize that it has taken some serious damage, and I want to know how can I tidy it up, without losing all my installed apps and configuration files.

  • Each of those are unrelated problems, you should convert them to individual questions. – João Pinto Nov 26 '10 at 8:22
  • @João Pinto I thought maybe I can fix them all at once somehow. – Gabi Purcaru Nov 26 '10 at 8:29
  • Just some hints, you can't fix errors on mounted filesystems, use a Live-System for that. The Transmission problem sounds like you've set a rule in DevilSpy or a similar program. And lastly you could try to move your gconf-files, mv .gconf .gconf_backup. And I agree with João, you should split it up so that it can be easier answered and is also search-friendlier. – Bobby Nov 26 '10 at 9:10
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    Most worries me file check errors on boot-up. These can indicate a harddisk failure. It may be the best time to backup your system (at least /home) now. After that I'd check your harddisk first before doing anything else. – Takkat Nov 26 '10 at 9:41
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    They are all problems with different scopes, representing different risks and requiring different course of actions, you can't fix them all with a single action. Also it is not clear that any of those problems results from the development stage. – João Pinto Nov 26 '10 at 10:04

I suggest you to backup your data in /home (using Deja Dup for example) into an external drive or other partition.

deja-dup Install deja-dup

Then save the list of installed packages:

dpkg --get-selections > ~/my-packages

and copy my-packages in a pen drive.

Then reinstall the system from fresh, and restore your applications:

sudo dpkg --set-selections < my-packages && sudo apt-get dselect-upgrade

This will download all the package and install it again.

Then you just have to restore your data backup and you're done!

Useful Links:

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  • didn't know about the dpkg --get-selections. thanks a lot. I will try this! – Gabi Purcaru Nov 26 '10 at 18:51

If you are using OpenNingia's method, don't forget to also backup your /etc/apt/sources.list and /etc/apt/sources.list.d and then restore them after installation. After doing that, run

sudo apt-get update

before importing selections via dpkg.

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Check with dmesg if your disk has I/O errors. If it does you need to make a backup of /home now!

If your disk is ok, you have two options:

  1. try copying your settings to a backup folder and restart

  2. make a clean reinstall and restore some of your settings

Option 1) For first option you create backup folder like my_backup and use command:

mv .??* my_backup

that will move all files that contain your settings (they start with a dot (.*)) to your backup folder.

Option 2) if option 1 didn't work do a fresh reinstall and leave data on home.
It's the best thing to do when you have multiple problems you can't solve. It doesn't take long and you solve your problems.

Do the step 1 (make sure you don't overwrite your original settings in backup if you have done step 1 before, in that case just remove newly created settings.). Reboot and at install make sure you select same partitions for root (/) and /home, then check root for format but leave data on /home. After install you can copy settings for each application you think is okay back to your /home. And create same user name so the backup will stay in your home folder.

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